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Bio::DB::Flat(3)      User Contributed Perl Documentation     Bio::DB::Flat(3)

NAME
       Bio::DB::Flat - Interface for indexed flat files

SYNOPSIS
	 $db = Bio::DB::Flat->new(-directory  => '/usr/share/embl',
				  -dbname     => 'mydb',
				  -format     => 'embl',
				  -index      => 'bdb',
				  -write_flag => 1);
	 $db->build_index('/usr/share/embl/primate.embl',
			  '/usr/share/embl/protists.embl');
	 $seq	    = $db->get_Seq_by_id('HSFOS');
	 @sequences = $db->get_Seq_by_acc('DIV'	=> 'primate');
	 $raw	    = $db->fetch_raw('HSFOS');

DESCRIPTION
       This object provides the	basic mechanism	to associate positions in
       files with primary and secondary	name spaces. Unlike
       Bio::Index::Abstract (see Bio::Index::Abstract),	this is	specialized to
       work with the "flat index" and BerkeleyDB indexed flat file formats
       worked out at the 2002 BioHackathon.

       This object is a	general	front end to the underlying databases.

FEEDBACK
   Mailing Lists
       User feedback is	an integral part of the	evolution of this and other
       Bioperl modules.	Send your comments and suggestions preferably to one
       of the Bioperl mailing lists.  Your participation is much appreciated.

	 bioperl-l@bioperl.org			- General discussion
	 http://bioperl.org/wiki/Mailing_lists	- About	the mailing lists

   Support
       Please direct usage questions or	support	issues to the mailing list:

       bioperl-l@bioperl.org

       rather than to the module maintainer directly. Many experienced and
       reponsive experts will be able look at the problem and quickly address
       it. Please include a thorough description of the	problem	with code and
       data examples if	at all possible.

   Reporting Bugs
       Report bugs to the Bioperl bug tracking system to help us keep track
       the bugs	and their resolution.  Bug reports can be submitted via	the
       web:

	 https://github.com/bioperl/bioperl-live/issues

AUTHOR - Lincoln Stein
       Email - lstein@cshl.org

APPENDIX
       The rest	of the documentation details each of the object	methods.
       Internal	methods	are usually preceded with an "_" (underscore).

   new
	Title	: new
	Usage	: my $db = Bio::DB::Flat->new(
			    -directory	=> $root_directory,
			    -dbname	=> 'mydb',
			    -write_flag	=> 1,
			    -index	=> 'bdb',
			    -verbose	=> 0,
			    -out	=> 'outputfile',
			    -format	=> 'genbank');
	Function: create a new Bio::DB::Flat object
	Returns	: new Bio::DB::Flat object
	Args	: -directory	Root directory containing "config.dat"
		  -write_flag	If true, allows	creation/updating.
		  -verbose	Verbose	messages
		  -out		File to	write to when write_seq	invoked
		  -index	'bdb' or 'binarysearch'
	Status	: Public

       The required -directory argument	indicates where	the flat file indexes
       will be stored.	The build_index() and write_seq() methods will
       automatically create subdirectories of this root	directory.  Each
       subdirectory will contain a human-readable configuration	file named
       "config.dat" that specifies where the individual	indexes	are stored.

       The required -dbname argument gives a name to the database index.  The
       index files will	actually be stored in a	like-named subdirectory
       underneath the root directory.

       The -write_flag enables writing new entries into	the database as	well
       as the creation of the indexes.	By default the indexes will be opened
       read only.

       -index is one of	"bdb" or "binarysearch"	and indicates the type of
       index to	generate.  "bdb" corresponds to	Berkeley DB.  You *must* be
       using BerkeleyDB	version	2 or higher, and have the Perl BerkeleyDB
       extension installed (DB_File will *not* work). "binarysearch"
       corresponds to the OBDA "flat" indexed file.

       The -out	argument specifies the output file for writing objects created
       with write_seq().

       The -format argument specifies the format of the	input file or files.
       If the file suffix is one that Bioperl can already associate with a
       format then this	is optional.

   new_from_registry
	Title	: new_from_registry
	Usage	: $db =	Bio::DB::Flat->new_from_registry(%config)
	Function: creates a new	Bio::DB::Flat object in	a Bio::DB::Registry-
		  compatible fashion
	Returns	: new Bio::DB::Flat
	Args	: provided by the registry, see	below
	Status	: Public

       The following registry-configuration tags are recognized:

	 location     Root of the indexed flat file; corresponds to the	new() method's
		      -directory argument.

   fetch
	 Title	 : fetch
	 Usage	 : $index->fetch( $id )
	 Function: Returns a Bio::Seq object from the index
	 Example : $seq	= $index->fetch( 'dJ67B12' )
	 Returns : Bio::Seq object
	 Args	 : ID

       Deprecated.  Use	get_Seq_by_id instead.

   To Be Implemented in	Subclasses
       The following methods MUST be implemented by subclasses.

   May Be Overridden in	Subclasses
       The following methods MAY be overridden by subclasses.

perl v5.32.0			  2019-12-07		      Bio::DB::Flat(3)

NAME | SYNOPSIS | DESCRIPTION | FEEDBACK | AUTHOR - Lincoln Stein | APPENDIX

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